NM_001382567.1(STIM1):c.13G>A (p.Val5Ile) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 9, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002544321.2

Allele description [Variation Report for NM_001382567.1(STIM1):c.13G>A (p.Val5Ile)]

NM_001382567.1(STIM1):c.13G>A (p.Val5Ile)

Genes:

LOC130005165:ATAC-STARR-seq lymphoblastoid active region 4312 [Gene]
STIM1:stromal interaction molecule 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p15.4

Genomic location:

Preferred name:

NM_001382567.1(STIM1):c.13G>A (p.Val5Ile)

HGVS:

NC_000011.10:g.3856283G>A
NG_016277.1:g.5581G>A
NM_001277961.3:c.13G>A
NM_001277962.2:c.13G>A
NM_001382566.1:c.-84+867G>A
NM_001382567.1:c.13G>AMANE SELECT
NM_001382568.1:c.13G>A
NM_001382569.1:c.9G>A
NM_001382570.1:c.13G>A
NM_001382571.1:c.-225G>A
NM_001382572.1:c.13G>A
NM_001382573.1:c.-84+867G>A
NM_001382574.1:c.-84+1547G>A
NM_001382575.1:c.-84+1547G>A
NM_001382576.1:c.-84+1629G>A
NM_001382577.1:c.-84+867G>A
NM_001382578.1:c.-84+1547G>A
NM_001382579.1:c.-84+867G>A
NM_001382580.1:c.-220+1547G>A
NM_001382581.1:c.-220+1547G>A
NM_003156.4:c.13G>A
NP_001264890.1:p.Val5Ile
NP_001264891.1:p.Val5Ile
NP_001369496.1:p.Val5Ile
NP_001369497.1:p.Val5Ile
NP_001369498.1:p.Ala3=
NP_001369499.1:p.Val5Ile
NP_001369501.1:p.Val5Ile
NP_003147.2:p.Val5Ile
LRG_164t1:c.13G>A
LRG_164:g.5581G>A
NC_000011.9:g.3877513G>A
NM_003156.3:c.13G>A
NR_168436.1:n.620G>A
NR_168437.1:n.620G>A
NR_168438.1:n.620G>A

Protein change:

V5I

Links:

dbSNP: rs150529970

NCBI 1000 Genomes Browser:

rs150529970

Molecular consequence:

NM_001382571.1:c.-225G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001382566.1:c.-84+867G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001382573.1:c.-84+867G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001382574.1:c.-84+1547G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001382575.1:c.-84+1547G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001382576.1:c.-84+1629G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001382577.1:c.-84+867G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001382578.1:c.-84+1547G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001382579.1:c.-84+867G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001382580.1:c.-220+1547G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001382581.1:c.-220+1547G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001277961.3:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001277962.2:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382567.1:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382568.1:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382570.1:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382572.1:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_003156.4:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_168436.1:n.620G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_168437.1:n.620G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_168438.1:n.620G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001382569.1:c.9G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Stormorken syndrome (STRMK)
Synonyms:: THROMBOCYTOPATHY, ASPLENIA, AND MIOSIS
Identifiers:: MONDO: MONDO:0008497; MedGen: C1861451; Orphanet: 3204; OMIM: 185070

Name:: Combined immunodeficiency due to STIM1 deficiency
Synonyms:: Immune dysfunction with T-cell inactivation due to calcium entry defect 2; STIM1 DEFICIENCY; IMMUNODEFICIENCY 10
Identifiers:: MONDO: MONDO:0013008; MedGen: C2748557; Orphanet: 169090; Orphanet: 317430; OMIM: 612783

Name:: Myopathy with tubular aggregates (TAM)
Synonyms:: Tubular Aggregate Myopathy
Identifiers:: MONDO: MONDO:0008051; MedGen: C0410207; OMIM: PS160565

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003354039	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 9, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003354039

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 9, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003354039.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 5 of the STIM1 protein (p.Val5Ile). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with STIM1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1327793). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 28, 2024

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